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SimGenex: A System for Concisely Specifying Simulation of Biological Processes and Experimentation

Authors:
Anyela Camargo
Jan T. Kim

Keywords: Gene Regulatory Networks; Simulation; Systems Biology

Abstract:
Computational models enable advances in understanding essential features of living systems. Such models can be used to simulate data that can also be measured empirically. Generating such simulated data is frequently a key step in developing and validating models. However, precisely specifying a complex procedure of simulating data is notoriously difficult. The SimGenex language reported here is designed to simplify this task as it is applicable in research scenarios where several candidate models are considered, the mathematical details of regulatory interactions are only known partially or described semiquantitatively, the majority of kinetic parameters are not empirically measured, and a gene expression matrix is available as a basis of identifying the best model. SimGenex enables succinct and flexible descriptions of simulating the biological processes and experimental procedures that are the building blocks of most current wet lab experimental protocols. It enables specification of reproducibly executable workflows for validating computational models of biological systems, it facilitates pre-processing and transformation of data as it is frequently applied in gene expression data analysis and it provides support for comparing and discriminating alternative candidate models based on their ability to approximate the empirical dataset. The result of applying a SimGenex program to a computational model is a simulated dataset that can directly be compared to empirically measured omic data through the specification of a distance measure which can be used to discriminate the best model among a number of candidates.

Pages: 26 to 30

Copyright: Copyright (c) IARIA, 2011

Publication date: May 22, 2011

Published in: conference

ISSN: 2308-4383

ISBN: 978-1-61208-137-3

Location: Venice/Mestre, Italy

Dates: from May 22, 2011 to May 27, 2011